Multiple sequence alignment - TraesCS5D01G123900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G123900 chr5D 100.000 2560 0 0 1 2560 184450025 184452584 0.000000e+00 4728.0
1 TraesCS5D01G123900 chr5D 88.608 1027 77 25 3 993 392943149 392944171 0.000000e+00 1212.0
2 TraesCS5D01G123900 chr5D 94.384 552 24 3 1681 2226 403968857 403969407 0.000000e+00 841.0
3 TraesCS5D01G123900 chr5D 97.264 329 7 2 2234 2560 375001229 375001557 8.000000e-155 556.0
4 TraesCS5D01G123900 chr5D 98.039 51 1 0 1607 1657 403968808 403968858 3.510000e-14 89.8
5 TraesCS5D01G123900 chr2A 92.553 2605 139 14 4 2560 478452560 478455157 0.000000e+00 3685.0
6 TraesCS5D01G123900 chr2A 94.333 1694 85 8 873 2560 33475005 33473317 0.000000e+00 2586.0
7 TraesCS5D01G123900 chr2A 89.497 914 50 12 4 875 33484239 33483330 0.000000e+00 1114.0
8 TraesCS5D01G123900 chr2D 90.903 1440 89 17 4 1403 382042124 382040687 0.000000e+00 1895.0
9 TraesCS5D01G123900 chr2D 90.826 218 13 5 1398 1608 382032118 382031901 4.170000e-73 285.0
10 TraesCS5D01G123900 chr6D 91.398 1395 90 17 4 1370 32220940 32219548 0.000000e+00 1884.0
11 TraesCS5D01G123900 chr6D 92.987 713 44 6 3 714 396275814 396276521 0.000000e+00 1035.0
12 TraesCS5D01G123900 chr6D 89.671 213 14 3 1404 1608 32219551 32219339 5.430000e-67 265.0
13 TraesCS5D01G123900 chr3A 95.955 1162 45 2 1400 2559 117788799 117787638 0.000000e+00 1884.0
14 TraesCS5D01G123900 chr3A 90.867 1292 91 16 4 1278 117790639 117789358 0.000000e+00 1707.0
15 TraesCS5D01G123900 chr1A 95.296 744 33 2 1819 2560 205552106 205552849 0.000000e+00 1179.0
16 TraesCS5D01G123900 chr1A 93.874 555 25 3 1681 2226 30575206 30575760 0.000000e+00 828.0
17 TraesCS5D01G123900 chr1A 96.078 51 2 0 1607 1657 30575157 30575207 1.630000e-12 84.2
18 TraesCS5D01G123900 chr5B 93.671 711 45 0 4 714 406162404 406161694 0.000000e+00 1064.0
19 TraesCS5D01G123900 chr1B 89.450 872 40 16 544 1378 561931884 561932740 0.000000e+00 1053.0
20 TraesCS5D01G123900 chr1B 92.214 655 28 8 734 1378 538800532 538799891 0.000000e+00 905.0
21 TraesCS5D01G123900 chr1B 93.841 552 28 2 1681 2226 159088419 159087868 0.000000e+00 826.0
22 TraesCS5D01G123900 chr1B 100.000 48 0 0 1610 1657 159088465 159088418 3.510000e-14 89.8
23 TraesCS5D01G123900 chr3B 93.268 713 45 2 4 714 342719834 342720545 0.000000e+00 1048.0
24 TraesCS5D01G123900 chr3B 88.761 872 49 15 544 1378 89341136 89341995 0.000000e+00 1022.0
25 TraesCS5D01G123900 chr3B 91.549 71 6 0 1537 1607 707599384 707599314 5.830000e-17 99.0
26 TraesCS5D01G123900 chr2B 90.746 778 61 8 842 1608 425736683 425737460 0.000000e+00 1027.0
27 TraesCS5D01G123900 chr1D 92.825 669 37 4 713 1370 407141595 407142263 0.000000e+00 959.0
28 TraesCS5D01G123900 chr1D 94.255 557 21 2 1681 2226 26249888 26249332 0.000000e+00 841.0
29 TraesCS5D01G123900 chr1D 90.657 578 22 4 1681 2226 463400286 463400863 0.000000e+00 739.0
30 TraesCS5D01G123900 chr1D 97.264 329 6 3 2234 2560 393952924 393952597 2.880000e-154 555.0
31 TraesCS5D01G123900 chr1D 86.463 229 24 1 1381 1602 407142419 407142647 7.080000e-61 244.0
32 TraesCS5D01G123900 chr1D 100.000 48 0 0 1610 1657 26249934 26249887 3.510000e-14 89.8
33 TraesCS5D01G123900 chr5A 88.889 756 72 4 716 1460 432750114 432749360 0.000000e+00 920.0
34 TraesCS5D01G123900 chr5A 97.183 426 10 2 2121 2544 580528810 580529235 0.000000e+00 719.0
35 TraesCS5D01G123900 chr4D 94.333 547 30 1 1681 2226 143275909 143276455 0.000000e+00 837.0
36 TraesCS5D01G123900 chr4D 93.357 557 26 2 1681 2226 275234085 275234641 0.000000e+00 813.0
37 TraesCS5D01G123900 chr4D 97.917 48 1 0 1610 1657 143275863 143275910 1.630000e-12 84.2
38 TraesCS5D01G123900 chr7A 97.418 426 9 2 2121 2544 75694466 75694891 0.000000e+00 725.0
39 TraesCS5D01G123900 chr7A 96.714 426 12 2 2121 2544 557426347 557425922 0.000000e+00 708.0
40 TraesCS5D01G123900 chr7B 85.647 634 76 10 985 1608 439175782 439175154 0.000000e+00 652.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G123900 chr5D 184450025 184452584 2559 False 4728.0 4728 100.0000 1 2560 1 chr5D.!!$F1 2559
1 TraesCS5D01G123900 chr5D 392943149 392944171 1022 False 1212.0 1212 88.6080 3 993 1 chr5D.!!$F3 990
2 TraesCS5D01G123900 chr5D 403968808 403969407 599 False 465.4 841 96.2115 1607 2226 2 chr5D.!!$F4 619
3 TraesCS5D01G123900 chr2A 478452560 478455157 2597 False 3685.0 3685 92.5530 4 2560 1 chr2A.!!$F1 2556
4 TraesCS5D01G123900 chr2A 33473317 33475005 1688 True 2586.0 2586 94.3330 873 2560 1 chr2A.!!$R1 1687
5 TraesCS5D01G123900 chr2A 33483330 33484239 909 True 1114.0 1114 89.4970 4 875 1 chr2A.!!$R2 871
6 TraesCS5D01G123900 chr2D 382040687 382042124 1437 True 1895.0 1895 90.9030 4 1403 1 chr2D.!!$R2 1399
7 TraesCS5D01G123900 chr6D 32219339 32220940 1601 True 1074.5 1884 90.5345 4 1608 2 chr6D.!!$R1 1604
8 TraesCS5D01G123900 chr6D 396275814 396276521 707 False 1035.0 1035 92.9870 3 714 1 chr6D.!!$F1 711
9 TraesCS5D01G123900 chr3A 117787638 117790639 3001 True 1795.5 1884 93.4110 4 2559 2 chr3A.!!$R1 2555
10 TraesCS5D01G123900 chr1A 205552106 205552849 743 False 1179.0 1179 95.2960 1819 2560 1 chr1A.!!$F1 741
11 TraesCS5D01G123900 chr1A 30575157 30575760 603 False 456.1 828 94.9760 1607 2226 2 chr1A.!!$F2 619
12 TraesCS5D01G123900 chr5B 406161694 406162404 710 True 1064.0 1064 93.6710 4 714 1 chr5B.!!$R1 710
13 TraesCS5D01G123900 chr1B 561931884 561932740 856 False 1053.0 1053 89.4500 544 1378 1 chr1B.!!$F1 834
14 TraesCS5D01G123900 chr1B 538799891 538800532 641 True 905.0 905 92.2140 734 1378 1 chr1B.!!$R1 644
15 TraesCS5D01G123900 chr1B 159087868 159088465 597 True 457.9 826 96.9205 1610 2226 2 chr1B.!!$R2 616
16 TraesCS5D01G123900 chr3B 342719834 342720545 711 False 1048.0 1048 93.2680 4 714 1 chr3B.!!$F2 710
17 TraesCS5D01G123900 chr3B 89341136 89341995 859 False 1022.0 1022 88.7610 544 1378 1 chr3B.!!$F1 834
18 TraesCS5D01G123900 chr2B 425736683 425737460 777 False 1027.0 1027 90.7460 842 1608 1 chr2B.!!$F1 766
19 TraesCS5D01G123900 chr1D 463400286 463400863 577 False 739.0 739 90.6570 1681 2226 1 chr1D.!!$F1 545
20 TraesCS5D01G123900 chr1D 407141595 407142647 1052 False 601.5 959 89.6440 713 1602 2 chr1D.!!$F2 889
21 TraesCS5D01G123900 chr1D 26249332 26249934 602 True 465.4 841 97.1275 1610 2226 2 chr1D.!!$R2 616
22 TraesCS5D01G123900 chr5A 432749360 432750114 754 True 920.0 920 88.8890 716 1460 1 chr5A.!!$R1 744
23 TraesCS5D01G123900 chr4D 275234085 275234641 556 False 813.0 813 93.3570 1681 2226 1 chr4D.!!$F1 545
24 TraesCS5D01G123900 chr4D 143275863 143276455 592 False 460.6 837 96.1250 1610 2226 2 chr4D.!!$F2 616
25 TraesCS5D01G123900 chr7B 439175154 439175782 628 True 652.0 652 85.6470 985 1608 1 chr7B.!!$R1 623

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
333 337 0.744874 CTTCCTACTGAATCGGCGGA 59.255 55.0 7.21 0.0 31.06 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 2354 1.208535 CCACGAGTAACCCATTGGCTA 59.791 52.381 0.0 0.0 33.59 3.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 214 6.808704 GCTAGTGGTTGAATCTTGGAATTTTC 59.191 38.462 0.00 0.00 0.00 2.29
294 298 1.362406 GAGCAAACTACGAGGCAGCC 61.362 60.000 1.84 1.84 0.00 4.85
298 302 2.725203 AAACTACGAGGCAGCCGCAA 62.725 55.000 16.28 1.39 41.24 4.85
333 337 0.744874 CTTCCTACTGAATCGGCGGA 59.255 55.000 7.21 0.00 31.06 5.54
389 393 4.559862 TTTGACACCCAACCATTTTGTT 57.440 36.364 0.00 0.00 33.85 2.83
616 623 2.251409 TAGAGACCGTCGGATACTGG 57.749 55.000 20.51 0.00 0.00 4.00
714 721 1.067060 TGTCGTTGAGGACACTGACAG 59.933 52.381 0.00 0.00 41.76 3.51
913 1015 3.775654 CCGCTCCTCCTCGCCTTT 61.776 66.667 0.00 0.00 0.00 3.11
933 1035 2.997897 GGACGACCACCTGCTCCT 60.998 66.667 0.00 0.00 35.97 3.69
1142 1248 1.970639 CCAGATCCTCGATGGCGAT 59.029 57.895 0.00 0.00 46.80 4.58
1189 1295 2.055042 CAGGTCCGTCTCCTCCCAG 61.055 68.421 0.00 0.00 32.37 4.45
1190 1296 3.462678 GGTCCGTCTCCTCCCAGC 61.463 72.222 0.00 0.00 0.00 4.85
1438 1984 2.180769 CGTCCTCACGCGGATTCA 59.819 61.111 12.47 0.00 39.69 2.57
1583 2136 0.176680 CGTGGTGAGATTCCCCTCTG 59.823 60.000 0.00 0.00 34.38 3.35
1592 2145 0.846427 ATTCCCCTCTGTGCCTCCAA 60.846 55.000 0.00 0.00 0.00 3.53
1595 2148 0.918983 CCCCTCTGTGCCTCCAAATA 59.081 55.000 0.00 0.00 0.00 1.40
1608 2161 5.106317 TGCCTCCAAATACAAATCGAAGTTC 60.106 40.000 0.00 0.00 0.00 3.01
1701 2254 4.566545 TTGTGTCAATGCAACCTTAGTG 57.433 40.909 0.00 0.00 0.00 2.74
1942 2511 1.298563 CCTGCAACACAGCACAACG 60.299 57.895 0.00 0.00 45.78 4.10
2092 2680 1.544691 ACTACGCGTCTTCATCCACTT 59.455 47.619 18.63 0.00 0.00 3.16
2332 2923 6.228616 TGATGTCCGTGTTTATCCAGATTA 57.771 37.500 0.00 0.00 0.00 1.75
2553 3145 5.488341 TGTAATCCTTCCTGTTCTACTTGC 58.512 41.667 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.427276 TGTTCTCAGAAATGAGCTATCATGTAT 58.573 33.333 0.00 0.00 45.67 2.29
285 289 2.198906 TTTGAATTGCGGCTGCCTCG 62.199 55.000 16.57 5.46 41.78 4.63
294 298 1.389784 GCGGGTCAAATTTGAATTGCG 59.610 47.619 22.07 0.67 39.21 4.85
298 302 3.165071 AGGAAGCGGGTCAAATTTGAAT 58.835 40.909 22.07 5.22 39.21 2.57
333 337 6.544928 ACCTCTGGTGAAAAAGACAAATTT 57.455 33.333 0.00 0.00 32.98 1.82
389 393 8.704849 ACTAGGCCATATTTAATGCACAATTA 57.295 30.769 5.01 0.00 0.00 1.40
616 623 0.743345 GTGTGGGCCGTTGGATCTAC 60.743 60.000 0.00 0.00 0.00 2.59
714 721 3.044059 GCATTCGGCCACTGACAGC 62.044 63.158 2.24 0.00 36.11 4.40
877 971 2.610859 TTGAGGTGGGAGGGGAGC 60.611 66.667 0.00 0.00 0.00 4.70
1162 1268 1.275291 GAGACGGACCTGATTTGACCA 59.725 52.381 0.00 0.00 0.00 4.02
1165 1271 1.825474 GAGGAGACGGACCTGATTTGA 59.175 52.381 0.00 0.00 37.93 2.69
1189 1295 1.986698 TCGCCAGTAAAACGACTAGC 58.013 50.000 0.00 0.00 31.57 3.42
1190 1296 4.724036 GCAAATCGCCAGTAAAACGACTAG 60.724 45.833 0.00 0.00 38.85 2.57
1438 1984 1.831652 CTGCTTTGGGAGGAGGACGT 61.832 60.000 0.00 0.00 39.93 4.34
1535 2088 2.273776 GGGAAGAGGAAGCAGCCC 59.726 66.667 0.00 0.00 0.00 5.19
1583 2136 4.156008 ACTTCGATTTGTATTTGGAGGCAC 59.844 41.667 0.00 0.00 0.00 5.01
1595 2148 8.668510 ATGCATATAGAAGAACTTCGATTTGT 57.331 30.769 19.46 7.25 43.97 2.83
1608 2161 6.370994 CAGTGGAGGCTAAATGCATATAGAAG 59.629 42.308 0.00 0.00 45.15 2.85
1701 2254 1.412710 TCTGGGAACGATGGTATCTGC 59.587 52.381 0.00 0.00 0.00 4.26
1801 2354 1.208535 CCACGAGTAACCCATTGGCTA 59.791 52.381 0.00 0.00 33.59 3.93
1942 2511 1.808945 GGATGCATGCACTATACCAGC 59.191 52.381 25.37 0.00 0.00 4.85
2092 2680 1.214325 CGTAGCGTGTGTCCATCCA 59.786 57.895 0.00 0.00 0.00 3.41
2103 2691 7.140705 TGTATACTACATAAAATGCGTAGCGT 58.859 34.615 4.17 0.00 46.65 5.07
2332 2923 6.518493 AGAATGTTGCAATCAAACATTCTGT 58.482 32.000 29.65 15.66 45.65 3.41
2412 3004 3.837213 TTAAATCAGCAGCAGCAACTC 57.163 42.857 3.17 0.00 45.49 3.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.